aligncommand.cpp

   1 /*
   2  *  aligncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 5/15/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  *      This version of nast does everything I think that the greengenes nast server does and then some.  I have added the
   9  *      feature of allowing users to define their database, kmer size for searching, alignment penalty values and alignment
  10  *      method.  This latter feature is perhaps most significant.  nastPlus enables a user to use either a Needleman-Wunsch
  11  *      (non-affine gap penalty) or Gotoh (affine gap penalty) pairwise alignment algorithm.  This is significant because it
  12  *      allows for a global alignment and not the local alignment provided by bLAst.  Furthermore, it has the potential to
  13  *      provide a better alignment because of the banding method employed by blast (I'm not sure about this).
  14  *
  15  */
  16
  17 #include "aligncommand.h"
  18 #include "sequence.hpp"
  19
  20 #include "gotohoverlap.hpp"
  21 #include "needlemanoverlap.hpp"
  22 #include "blastalign.hpp"
  23 #include "noalign.hpp"
  24
  25 #include "nast.hpp"
  26 #include "nastreport.hpp"
  27
  28 //**********************************************************************************************************************
  29 vector<string> AlignCommand::setParameters(){
  30         try {
  31                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
  32                 CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcandidate);
  33                 CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "",false,false); parameters.push_back(psearch);
  34                 CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
  35                 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
  36                 CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
  37                 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
  38                 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
  39                 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
  40                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  41                 CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
  42                 CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(pthreshold);
  43                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  44                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  45
  46                 vector<string> myArray;
  47                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  48                 return myArray;
  49         }
  50         catch(exception& e) {
  51                 m->errorOut(e, "AlignCommand", "setParameters");
  52                 exit(1);
  53         }
  54 }
  55 //**********************************************************************************************************************
  56 string AlignCommand::getHelpString(){
  57         try {
  58                 string helpString = "";
  59                 helpString += "The align.seqs command reads a file containing sequences and creates an alignment file and a report file.";
  60                 helpString += "The align.seqs command parameters are reference, fasta, search, ksize, align, match, mismatch, gapopen, gapextend and processors.";
  61                 helpString += "The reference and fasta parameters are required. You may leave fasta blank if you have a valid fasta file. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta.";
  62                 helpString += "The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer and blast. The default is kmer.";
  63                 helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.";
  64                 helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.";
  65                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.";
  66                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.";
  67                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.";
  68                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.";
  69                 helpString += "The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold.  The default is false.";
  70                 helpString += "The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.";
  71                 helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.";
  72                 helpString += "The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.";
  73                 helpString += "The align.seqs command should be in the following format:";
  74                 helpString += "align.seqs(reference=yourTemplateFile, fasta=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty)";
  75                 helpString += "Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)";
  76                 helpString += "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).";
  77                 return helpString;
  78         }
  79         catch(exception& e) {
  80                 m->errorOut(e, "AlignCommand", "getHelpString");
  81                 exit(1);
  82         }
  83 }
  84 //**********************************************************************************************************************
  85 AlignCommand::AlignCommand(){
  86         try {
  87                 abort = true; calledHelp = true;
  88                 setParameters();
  89                 vector<string> tempOutNames;
  90                 outputTypes["fasta"] = tempOutNames;
  91                 outputTypes["alignreport"] = tempOutNames;
  92                 outputTypes["accnos"] = tempOutNames;
  93         }
  94         catch(exception& e) {
  95                 m->errorOut(e, "AlignCommand", "AlignCommand");
  96                 exit(1);
  97         }
  98 }
  99 //**********************************************************************************************************************
 100 AlignCommand::AlignCommand(string option)  {
 101         try {
 102                 abort = false; calledHelp = false;
 103
 104                 //allow user to run help
 105                 if(option == "help") { help(); abort = true; calledHelp = true;}
 106
 107                 else {
 108                         vector<string> myArray = setParameters();
 109
 110                         OptionParser parser(option);
 111                         map<string, string> parameters = parser.getParameters();
 112
 113                         ValidParameters validParameter("align.seqs");
 114                         map<string, string>::iterator it;
 115
 116                         //check to make sure all parameters are valid for command
 117                         for (it = parameters.begin(); it != parameters.end(); it++) {
 118                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 119                         }
 120
 121                         //initialize outputTypes
 122                         vector<string> tempOutNames;
 123                         outputTypes["fasta"] = tempOutNames;
 124                         outputTypes["alignreport"] = tempOutNames;
 125                         outputTypes["accnos"] = tempOutNames;
 126
 127                         //if the user changes the output directory command factory will send this info to us in the output parameter
 128                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 129
 130
 131                         //if the user changes the input directory command factory will send this info to us in the output parameter
 132                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 133
 134                         if (inputDir == "not found"){   inputDir = "";          }
 135                         else {
 136                                 string path;
 137
 138                                 it = parameters.find("reference");
 139
 140                                 //user has given a template file
 141                                 if(it != parameters.end()){
 142                                         path = m->hasPath(it->second);
 143                                         //if the user has not given a path then, add inputdir. else leave path alone.
 144                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 145                                 }
 146                         }
 147
 148                         //check for required parameters
 149                         templateFileName = validParameter.validFile(parameters, "reference", true);
 150
 151                         if (templateFileName == "not found") {
 152                                 m->mothurOut("reference is a required parameter for the align.seqs command.");
 153                                 m->mothurOutEndLine();
 154                                 abort = true;
 155                         }else if (templateFileName == "not open") { abort = true; }
 156
 157                         candidateFileName = validParameter.validFile(parameters, "fasta", false);
 158                         if (candidateFileName == "not found") {
 159                                 //if there is a current fasta file, use it
 160                                 string filename = m->getFastaFile();
 161                                 if (filename != "") { candidateFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 162                                 else {  m->mothurOut("You have no current fastafile and the candidate parameter is required."); m->mothurOutEndLine(); abort = true; }
 163                         }else {
 164                                 m->splitAtDash(candidateFileName, candidateFileNames);
 165
 166                                 //go through files and make sure they are good, if not, then disregard them
 167                                 for (int i = 0; i < candidateFileNames.size(); i++) {
 168                                         //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
 169
 170                                         if (inputDir != "") {
 171                                                 string path = m->hasPath(candidateFileNames[i]);
 172                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 173                                                 if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }
 174                                         }
 175
 176                                         int ableToOpen;
 177                                         ifstream in;
 178                                         ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
 179                                         in.close();
 180
 181                                         //if you can't open it, try default location
 182                                         if (ableToOpen == 1) {
 183                                                 if (m->getDefaultPath() != "") { //default path is set
 184                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
 185                                                         m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 186                                                         ifstream in2;
 187                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 188                                                         in2.close();
 189                                                         candidateFileNames[i] = tryPath;
 190                                                 }
 191                                         }
 192
 193                                         //if you can't open it, try output location
 194                                         if (ableToOpen == 1) {
 195                                                 if (m->getOutputDir() != "") { //default path is set
 196                                                         string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
 197                                                         m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 198                                                         ifstream in2;
 199                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 200                                                         in2.close();
 201                                                         candidateFileNames[i] = tryPath;
 202                                                 }
 203                                         }
 204
 205
 206
 207                                         if (ableToOpen == 1) {
 208                                                 m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 209                                                 //erase from file list
 210                                                 candidateFileNames.erase(candidateFileNames.begin()+i);
 211                                                 i--;
 212                                         }
 213
 214                                 }
 215
 216                                 //make sure there is at least one valid file left
 217                                 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 218                         }
 219
 220                         //check for optional parameter and set defaults
 221                         // ...at some point should added some additional type checking...
 222                         string temp;
 223                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 224                         convert(temp, kmerSize);
 225
 226                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 227                         convert(temp, match);
 228
 229                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 230                         convert(temp, misMatch);
 231
 232                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 233                         convert(temp, gapOpen);
 234
 235                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 236                         convert(temp, gapExtend);
 237
 238                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 239                         m->setProcessors(temp);
 240                         convert(temp, processors);
 241
 242                         temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
 243                         flip = m->isTrue(temp);
 244
 245                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
 246                         convert(temp, threshold);
 247
 248                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 249                         if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
 250
 251                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 252                         if ((align != "needleman") && (align != "gotoh") && (align != "blast") && (align != "noalign")) { m->mothurOut("invalid align option: choices are needleman, gotoh, blast or noalign."); m->mothurOutEndLine(); abort=true; }
 253
 254                 }
 255
 256         }
 257         catch(exception& e) {
 258                 m->errorOut(e, "AlignCommand", "AlignCommand");
 259                 exit(1);
 260         }
 261 }
 262 //**********************************************************************************************************************
 263 AlignCommand::~AlignCommand(){
 264
 265         if (abort == false) {
 266                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 267                 delete templateDB;
 268                 delete alignment;
 269         }
 270 }
 271 //**********************************************************************************************************************
 272
 273 int AlignCommand::execute(){
 274         try {
 275                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 276
 277                 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
 278                 int longestBase = templateDB->getLongestBase();
 279
 280                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 281                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 282                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 283                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 284                 else {
 285                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 286                         m->mothurOutEndLine();
 287                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 288                 }
 289
 290                 for (int s = 0; s < candidateFileNames.size(); s++) {
 291                         if (m->control_pressed) { outputTypes.clear(); return 0; }
 292
 293                         m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
 294
 295                         if (outputDir == "") {  outputDir += m->hasPath(candidateFileNames[s]); }
 296                         string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
 297                         string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
 298                         string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
 299                         bool hasAccnos = true;
 300
 301                         int numFastaSeqs = 0;
 302                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 303                         int start = time(NULL);
 304
 305 #ifdef USE_MPI
 306                                 int pid, numSeqsPerProcessor;
 307                                 int tag = 2001;
 308                                 vector<unsigned long int> MPIPos;
 309                                 MPIWroteAccnos = false;
 310
 311                                 MPI_Status status;
 312                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 313                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 314
 315                                 MPI_File inMPI;
 316                                 MPI_File outMPIAlign;
 317                                 MPI_File outMPIReport;
 318                                 MPI_File outMPIAccnos;
 319
 320                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 321                                 int inMode=MPI_MODE_RDONLY;
 322
 323                                 char outAlignFilename[1024];
 324                                 strcpy(outAlignFilename, alignFileName.c_str());
 325
 326                                 char outReportFilename[1024];
 327                                 strcpy(outReportFilename, reportFileName.c_str());
 328
 329                                 char outAccnosFilename[1024];
 330                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 331
 332                                 char inFileName[1024];
 333                                 strcpy(inFileName, candidateFileNames[s].c_str());
 334
 335                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 336                                 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
 337                                 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
 338                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 339
 340                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 341
 342                                 if (pid == 0) { //you are the root process
 343
 344                                         MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 345
 346                                         //send file positions to all processes
 347                                         for(int i = 1; i < processors; i++) {
 348                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 349                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 350                                         }
 351
 352                                         //figure out how many sequences you have to align
 353                                         numSeqsPerProcessor = numFastaSeqs / processors;
 354                                         int startIndex =  pid * numSeqsPerProcessor;
 355                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 356
 357                                         //align your part
 358                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 359
 360                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 361
 362                                         for (int i = 1; i < processors; i++) {
 363                                                 bool tempResult;
 364                                                 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 365                                                 if (tempResult != 0) { MPIWroteAccnos = true; }
 366                                         }
 367                                 }else{ //you are a child process
 368                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 369                                         MPIPos.resize(numFastaSeqs+1);
 370                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 371
 372
 373                                         //figure out how many sequences you have to align
 374                                         numSeqsPerProcessor = numFastaSeqs / processors;
 375                                         int startIndex =  pid * numSeqsPerProcessor;
 376                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 377
 378
 379                                         //align your part
 380                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 381
 382                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 383
 384                                         MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 385                                 }
 386
 387                                 //close files
 388                                 MPI_File_close(&inMPI);
 389                                 MPI_File_close(&outMPIAlign);
 390                                 MPI_File_close(&outMPIReport);
 391                                 MPI_File_close(&outMPIAccnos);
 392
 393                                 //delete accnos file if blank
 394                                 if (pid == 0) {
 395                                         //delete accnos file if its blank else report to user
 396                                         if (MPIWroteAccnos) {
 397                                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 398                                                 if (!flip) {
 399                                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 400                                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 401                                                 m->mothurOutEndLine();
 402                                         }else {
 403                                                 //MPI_Info info;
 404                                                 //MPI_File_delete(outAccnosFilename, info);
 405                                                 hasAccnos = false;
 406                                                 remove(accnosFileName.c_str());
 407                                         }
 408                                 }
 409
 410 #else
 411
 412                 vector<unsigned long int> positions = m->divideFile(candidateFileNames[s], processors);
 413                 for (int i = 0; i < (positions.size()-1); i++) {
 414                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 415                 }
 416         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 417                         if(processors == 1){
 418                                 numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 419                         }else{
 420                                 numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 421                         }
 422         #else
 423                         numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 424         #endif
 425
 426                         if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear();  return 0; }
 427
 428                         //delete accnos file if its blank else report to user
 429                         if (m->isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 430                         else {
 431                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 432                                 if (!flip) {
 433                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 434                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 435                                 m->mothurOutEndLine();
 436                         }
 437
 438 #endif
 439
 440
 441                 #ifdef USE_MPI
 442                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 443
 444                         if (pid == 0) { //only one process should output to screen
 445                 #endif
 446
 447                         outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
 448                         outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
 449                         if (hasAccnos)  {       outputNames.push_back(accnosFileName);  outputTypes["accnos"].push_back(accnosFileName);  }
 450
 451                 #ifdef USE_MPI
 452                         }
 453                 #endif
 454
 455                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 456                         m->mothurOutEndLine();
 457                         m->mothurOutEndLine();
 458                 }
 459
 460                 //set align file as new current fastafile
 461                 string currentFasta = "";
 462                 itTypes = outputTypes.find("fasta");
 463                 if (itTypes != outputTypes.end()) {
 464                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 465                 }
 466
 467                 m->mothurOutEndLine();
 468                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 469                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 470                 m->mothurOutEndLine();
 471
 472                 return 0;
 473         }
 474         catch(exception& e) {
 475                 m->errorOut(e, "AlignCommand", "execute");
 476                 exit(1);
 477         }
 478 }
 479
 480 //**********************************************************************************************************************
 481
 482 int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
 483         try {
 484                 ofstream alignmentFile;
 485                 m->openOutputFile(alignFName, alignmentFile);
 486
 487                 ofstream accnosFile;
 488                 m->openOutputFile(accnosFName, accnosFile);
 489
 490                 NastReport report(reportFName);
 491
 492                 ifstream inFASTA;
 493                 m->openInputFile(filename, inFASTA);
 494
 495                 inFASTA.seekg(filePos->start);
 496
 497                 bool done = false;
 498                 int count = 0;
 499
 500                 while (!done) {
 501
 502                         if (m->control_pressed) {  return 0; }
 503
 504                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 505                         report.setCandidate(candidateSeq);
 506
 507                         int origNumBases = candidateSeq->getNumBases();
 508                         string originalUnaligned = candidateSeq->getUnaligned();
 509                         int numBasesNeeded = origNumBases * threshold;
 510
 511                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 512                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 513                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 514                                 }
 515
 516                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 517                                 Sequence* templateSeq = &temp;
 518
 519                                 float searchScore = templateDB->getSearchScore();
 520
 521                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 522
 523                                 Sequence* copy;
 524
 525                                 Nast* nast2;
 526                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 527                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 528                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 529                                                                                                 //so this bool tells you if you need to delete it
 530
 531                                 //if there is a possibility that this sequence should be reversed
 532                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 533
 534                                         string wasBetter =  "";
 535                                         //if the user wants you to try the reverse
 536                                         if (flip) {
 537
 538                                                 //get reverse compliment
 539                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 540                                                 copy->reverseComplement();
 541
 542                                                 //rerun alignment
 543                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 544                                                 Sequence* templateSeq2 = &temp2;
 545
 546                                                 searchScore = templateDB->getSearchScore();
 547
 548                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 549
 550                                                 //check if any better
 551                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 552                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 553                                                         templateSeq = templateSeq2;
 554                                                         delete nast;
 555                                                         nast = nast2;
 556                                                         needToDeleteCopy = true;
 557                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 558                                                 }else{
 559                                                         wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
 560                                                         delete nast2;
 561                                                         delete copy;
 562                                                 }
 563                                         }
 564
 565                                         //create accnos file with names
 566                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 567                                 }
 568
 569                                 report.setTemplate(templateSeq);
 570                                 report.setSearchParameters(search, searchScore);
 571                                 report.setAlignmentParameters(align, alignment);
 572                                 report.setNastParameters(*nast);
 573
 574                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 575
 576                                 report.print();
 577                                 delete nast;
 578                                 if (needToDeleteCopy) {   delete copy;   }
 579
 580                                 count++;
 581                         }
 582                         delete candidateSeq;
 583
 584                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 585                                 unsigned long int pos = inFASTA.tellg();
 586                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 587                         #else
 588                                 if (inFASTA.eof()) { break; }
 589                         #endif
 590
 591                         //report progress
 592                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 593
 594                 }
 595                 //report progress
 596                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 597
 598                 alignmentFile.close();
 599                 inFASTA.close();
 600                 accnosFile.close();
 601
 602                 return count;
 603         }
 604         catch(exception& e) {
 605                 m->errorOut(e, "AlignCommand", "driver");
 606                 exit(1);
 607         }
 608 }
 609 //**********************************************************************************************************************
 610 #ifdef USE_MPI
 611 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long int>& MPIPos){
 612         try {
 613                 string outputString = "";
 614                 MPI_Status statusReport;
 615                 MPI_Status statusAlign;
 616                 MPI_Status statusAccnos;
 617                 MPI_Status status;
 618                 int pid;
 619                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 620
 621                 NastReport report;
 622
 623                 if (pid == 0) {
 624                         outputString = report.getHeaders();
 625                         int length = outputString.length();
 626
 627                         char* buf = new char[length];
 628                         memcpy(buf, outputString.c_str(), length);
 629
 630                         MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
 631
 632             delete buf;
 633                 }
 634
 635                 for(int i=0;i<num;i++){
 636
 637                         if (m->control_pressed) {  return 0; }
 638
 639                         //read next sequence
 640                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 641
 642                         char* buf4 = new char[length];
 643                         //memcpy(buf4, outputString.c_str(), length);
 644
 645                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 646
 647                         string tempBuf = buf4;
 648
 649                         delete buf4;
 650
 651                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 652
 653                         istringstream iss (tempBuf,istringstream::in);
 654
 655                         Sequence* candidateSeq = new Sequence(iss);
 656                         report.setCandidate(candidateSeq);
 657
 658                         int origNumBases = candidateSeq->getNumBases();
 659                         string originalUnaligned = candidateSeq->getUnaligned();
 660                         int numBasesNeeded = origNumBases * threshold;
 661
 662                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 663                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 664                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 665                                 }
 666
 667                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 668                                 Sequence* templateSeq = &temp;
 669
 670                                 float searchScore = templateDB->getSearchScore();
 671
 672                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 673                                 Sequence* copy;
 674
 675                                 Nast* nast2;
 676                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 677                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 678                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 679                                                                                                 //so this bool tells you if you need to delete it
 680
 681                                 //if there is a possibility that this sequence should be reversed
 682                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 683
 684                                         string wasBetter = "";
 685                                         //if the user wants you to try the reverse
 686                                         if (flip) {
 687                                                 //get reverse compliment
 688                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 689                                                 copy->reverseComplement();
 690
 691                                                 //rerun alignment
 692                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 693                                                 Sequence* templateSeq2 = &temp2;
 694
 695                                                 searchScore = templateDB->getSearchScore();
 696
 697                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 698
 699                                                 //check if any better
 700                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 701                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 702                                                         templateSeq = templateSeq2;
 703                                                         delete nast;
 704                                                         nast = nast2;
 705                                                         needToDeleteCopy = true;
 706                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 707                                                 }else{
 708                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 709                                                         delete nast2;
 710                                                         delete copy;
 711                                                 }
 712                                         }
 713
 714                                         //create accnos file with names
 715                                         outputString = candidateSeq->getName() + wasBetter + "\n";
 716
 717                                         //send results to parent
 718                                         int length = outputString.length();
 719
 720                                         char* buf = new char[length];
 721                                         memcpy(buf, outputString.c_str(), length);
 722
 723                                         MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
 724                                         delete buf;
 725                                         MPIWroteAccnos = true;
 726                                 }
 727
 728                                 report.setTemplate(templateSeq);
 729                                 report.setSearchParameters(search, searchScore);
 730                                 report.setAlignmentParameters(align, alignment);
 731                                 report.setNastParameters(*nast);
 732
 733                                 outputString =  ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
 734
 735                                 //send results to parent
 736                                 int length = outputString.length();
 737                                 char* buf2 = new char[length];
 738                                 memcpy(buf2, outputString.c_str(), length);
 739
 740                                 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
 741
 742                                 delete buf2;
 743
 744                                 outputString = report.getReport();
 745
 746                                 //send results to parent
 747                                 length = outputString.length();
 748                                 char* buf3 = new char[length];
 749                                 memcpy(buf3, outputString.c_str(), length);
 750
 751                                 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
 752
 753                                 delete buf3;
 754                                 delete nast;
 755                                 if (needToDeleteCopy) {   delete copy;   }
 756                         }
 757                         delete candidateSeq;
 758
 759                         //report progress
 760                         if((i+1) % 100 == 0){   cout << (toString(i+1)) << endl;                }
 761                 }
 762                 //report progress
 763                 if((num) % 100 != 0){   cout << (toString(num)) << endl;                }
 764
 765                 return 1;
 766         }
 767         catch(exception& e) {
 768                 m->errorOut(e, "AlignCommand", "driverMPI");
 769                 exit(1);
 770         }
 771 }
 772 #endif
 773 /**************************************************************************************************/
 774
 775 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 776         try {
 777 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 778                 processIDS.resize(0);
 779                 int process = 1;
 780                 int num = 0;
 781                 //              processIDS.resize(0);
 782
 783                 //loop through and create all the processes you want
 784                 while (process != processors) {
 785                         int pid = fork();
 786
 787                         if (pid > 0) {
 788                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 789                                 process++;
 790                         }else if (pid == 0){
 791                                 num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 792
 793                                 //pass numSeqs to parent
 794                                 ofstream out;
 795                                 string tempFile = alignFileName + toString(getpid()) + ".num.temp";
 796                                 m->openOutputFile(tempFile, out);
 797                                 out << num << endl;
 798                                 out.close();
 799
 800                                 exit(0);
 801                         }else {
 802                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 803                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 804                                 exit(0);
 805                         }
 806                 }
 807
 808                 //do my part
 809                 num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);
 810
 811                 //force parent to wait until all the processes are done
 812                 for (int i=0;i<processIDS.size();i++) {
 813                         int temp = processIDS[i];
 814                         wait(&temp);
 815                 }
 816
 817                 vector<string> nonBlankAccnosFiles;
 818                 if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
 819                 else { remove(accnosFName.c_str()); } //remove so other files can be renamed to it
 820
 821                 for (int i = 0; i < processIDS.size(); i++) {
 822                         ifstream in;
 823                         string tempFile =  alignFileName + toString(processIDS[i]) + ".num.temp";
 824                         m->openInputFile(tempFile, in);
 825                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 826                         in.close(); remove(tempFile.c_str());
 827
 828                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 829                         remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
 830
 831                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 832                         remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
 833
 834                         if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
 835                                 nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
 836                         }else { remove((accnosFName + toString(processIDS[i]) + ".temp").c_str());  }
 837
 838                 }
 839
 840                 //append accnos files
 841                 if (nonBlankAccnosFiles.size() != 0) {
 842                         rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
 843
 844                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 845                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
 846                                 remove(nonBlankAccnosFiles[h].c_str());
 847                         }
 848                 }else { //recreate the accnosfile if needed
 849                         ofstream out;
 850                         m->openOutputFile(accnosFName, out);
 851                         out.close();
 852                 }
 853
 854                 return num;
 855 #endif
 856         }
 857         catch(exception& e) {
 858                 m->errorOut(e, "AlignCommand", "createProcesses");
 859                 exit(1);
 860         }
 861 }
 862 /**************************************************************************************************/
 863
 864 void AlignCommand::appendAlignFiles(string temp, string filename) {
 865         try{
 866
 867                 ofstream output;
 868                 ifstream input;
 869                 m->openOutputFileAppend(filename, output);
 870                 m->openInputFile(temp, input);
 871
 872                 while(char c = input.get()){
 873                         if(input.eof())         {       break;                  }
 874                         else                            {       output << c;    }
 875                 }
 876
 877                 input.close();
 878                 output.close();
 879         }
 880         catch(exception& e) {
 881                 m->errorOut(e, "AlignCommand", "appendAlignFiles");
 882                 exit(1);
 883         }
 884 }
 885 //**********************************************************************************************************************
 886
 887 void AlignCommand::appendReportFiles(string temp, string filename) {
 888         try{
 889
 890                 ofstream output;
 891                 ifstream input;
 892                 m->openOutputFileAppend(filename, output);
 893                 m->openInputFile(temp, input);
 894
 895                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
 896
 897                 while(char c = input.get()){
 898                         if(input.eof())         {       break;                  }
 899                         else                            {       output << c;    }
 900                 }
 901
 902                 input.close();
 903                 output.close();
 904         }
 905         catch(exception& e) {
 906                 m->errorOut(e, "AlignCommand", "appendReportFiles");
 907                 exit(1);
 908         }
 909 }
 910 //**********************************************************************************************************************